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120,247 results • Page
1 of 2405
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Votes
Replies
1
vote
1
reply
34
views
ChIPSeeker not annotating with hg38, stuck on hg19
CHiPseeker
ATAC-Seq
20 minutes ago by
John
• 0
0
votes
1
reply
14
views
I cannot obtain my counts in galaxy server
galaxy
updated 29 minutes ago by
Ram
44k • written 38 minutes ago by
Hossein
• 0
0
votes
1
reply
27
views
How well was the rRNA depletion for RNA-Seq experiments
contamination
star
rrna
bbduk
ribodetector
updated 47 minutes ago by
GenoMax
149k • written 2 hours ago by
gogeni5529
▴ 50
0
votes
3
replies
20
views
Illumina HumanHT-12 V4.0 analysis but I only have the .IDAT files
Illumina
Expression
Analysis
Microarray
just now by
isaac_mani
• 0
1
vote
0
replies
12
views
edgeR questions for use with cytometry counts
edgeR
cytometry
diffcyt
1 hour ago by
SamGG
▴ 90
0
votes
0
replies
17
views
scType on Xenium Spatial Transcriptomics
Spatial
Xenium
scType
updated 1 hour ago by
GenoMax
149k • written 1 hour ago by
Emma Jayne
• 0
6
votes
6
replies
148
views
6 follow
Analyze read lengths in Illumina data
human
illumina
libraries
updated 1 hour ago by
Pierre Lindenbaum
165k • written 8 hours ago by
María José
▴ 10
4
votes
3
replies
104
views
Convert Long Nanopore reads to Illumina Paired end reads
illumina
sequencing
reads
nanopore
updated 2 hours ago by
Pierre Lindenbaum
165k • written 5 hours ago by
Mark
▴ 30
825
votes
169
replies
165k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
3.3k • written 8.2 years ago by
Istvan Albert
102k
2
votes
0
replies
33
views
Tool:
AliNe (Alignment in Nextflow)
nextflow
alignment
2 hours ago by
Juke34
9.0k
0
votes
0
replies
37
views
(Too?) Simple Deep Mutational Sequencing pipeline for fastq to enrichment score
score
enrichment
deep
mutational
sequencing
4 hours ago by
Flipstone
• 0
0
votes
1
reply
58
views
Seeking Public Nanopore Datasets (FAST5 + FASTA/FASTQ) for DNA Storage Research
NanoporeSequencing
MachineLearning
DNA
FAST5
updated 4 hours ago by
GenoMax
149k • written 4 hours ago by
Dev
• 0
0
votes
3
replies
114
views
Umi_tools regex blank output
regex
umi_tools
47 minutes ago by
amyruthvandiver
• 0
0
votes
0
replies
40
views
RAxML or BV-BRC tree
RAxML
tree
Phylogenic
BV-BRC
7 hours ago by
anna
• 0
0
votes
0
replies
38
views
Choosing the better input files for COGclassifier tool
classifier
COG
7 hours ago by
anna
• 0
0
votes
0
replies
44
views
Anti-ligand , receptor blocking and cell cell interaction analysis
cellchat
cell
nichenet
single
7 hours ago by
carolofharvest
▴ 50
0
votes
0
replies
44
views
Gene ontology and NCBI blast analysis
protein
ontology
sequence
blast
gene
8 hours ago by
souparnika
• 0
0
votes
2
replies
122
views
Check the normalizations available in a hic file?
juicer-tools
hic-pro
hic
updated 10 hours ago by
Jim Robinson
▴ 300 • written 1 day ago by
rls_08
▴ 40
0
votes
0
replies
141
views
How can I linearize certain segments within an existing protein structure constraining to volumetric grids using PyMOL scripting?
structural-bioinformatics
protein
biopython
pymol
Python
10 hours ago by
Aman Vishwakarma
▴ 10
4
votes
5
replies
142
views
Overlapping regions in bedGraph
bedGraphToBigWig
bedGraph
updated 38 minutes ago by
Ram
44k • written 15 hours ago by
Aayush
• 0
3
votes
3
replies
1.2k
views
How to estimate and visualize haplotype blocks on a phased VCF/BCF
haplotype
vcf
updated 18 hours ago by
cmdcolin
★ 4.1k • written 2.2 years ago by
William
★ 5.3k
1
vote
3
replies
144
views
Low RIN, novel samples
RIN
RNA
4 hours ago by
Emilie
▴ 10
6
votes
7
replies
248
views
Why don't mRNA levels measure protein synthesis rates?
mRNA
translation
protein-synthesis
rnaseq
updated 14 hours ago by
Ram
44k • written 1 day ago by
Qroid
▴ 40
31
votes
13
replies
537
views
10 follow
Forum:
How do you estimate time to complete a project or task?
career
ngs
updated 4 hours ago by
GenoMax
149k • written 1 day ago by
sviatoslav.kendall
▴ 960
2
votes
9
replies
225
views
Drosophila melanogaster dm3 intron percentage too high
drosophila
sequence
nucleotide
intron
genomics
updated 2 hours ago by
Istvan Albert
102k • written 23 hours ago by
Christian
• 0
0
votes
3
replies
134
views
Finding high number of significant genes by FindMarkers by Seurat
FindMarkers
Single-cell
Seurat
updated 2 hours ago by
jared.andrews07
★ 18k • written 1 day ago by
Rosa Icela
• 0
1
vote
3
replies
168
views
What is the next step after getting the raw counts matrix for RNA-seq data?
DESEq2
transriptomics
RNA-seq
updated 4 hours ago by
Istvan Albert
102k • written 23 hours ago by
rajdeepboral00
▴ 20
3
votes
11
replies
2.2k
views
How can I linearize certain residues within an existing protein structure to create a dumbbell-shaped structure?
pymol
python
biopython
structural-bioinformatics
10 hours ago by
Aman Vishwakarma
▴ 10
0
votes
1
reply
991
views
codon adaptation index (CAI) estimation
codon-usage
updated 19 hours ago by
Ram
44k • written 5.3 years ago by
rthapa
▴ 90
0
votes
0
replies
92
views
Analysis of Illumina beadArray data
Illumina
biostatistics
transcriptomics
9 hours ago by
Ariadna
▴ 20
0
votes
3
replies
221
views
High adj. p-value/FDR despite large FC and high expression levels
edgeR
DESeq2
RNA-Seq
updated 1 day ago by
yura.grabovska
▴ 690 • written 1 day ago by
nik.kraemer
• 0
0
votes
1
reply
105
views
Why Is My Uniquely Mapped Read Count Higher in Samtools Compared to Bowtie2?
Bowtie2
updated 23 hours ago by
Istvan Albert
102k • written 1 day ago by
daffodil
▴ 10
0
votes
0
replies
74
views
XR-seq processing pipeline
XR-seq
1 day ago by
sleepystudent
• 0
0
votes
0
replies
84
views
Smart-Seq3 intron+exon meaning
exon
R
smart-seq3
plots
intron
1 day ago by
Evlampia
• 0
0
votes
0
replies
75
views
I'm not sure what is going on with my DEXSeq object
GenomicRanges
DEXSeq
Help
RNA-Seq
SummarizedExperiment
1 day ago by
cftattersfield
• 0
0
votes
1
reply
264
views
ChIP-seq signal across bed regions
normalisation
chipseq
quantification
signal
updated 1 day ago by
mark.ziemann
★ 2.0k • written 5 days ago by
SEJAL
• 0
2
votes
2
replies
265
views
Reading location of a feature of a miRNA entry in miRBase in EMBL format
format
miRBase
EMBL
1 day ago by
Coleman
• 0
0
votes
3
replies
213
views
How can you interpret a phased VCF with no "phase set" field (PS)
variants
vcf
phasing
genotyping
22 hours ago by
cmdcolin
★ 4.1k
2
votes
6
replies
434
views
How to make a .gaf file for GO analysis
NGS
GO
1 day ago by
noodle
▴ 620
0
votes
5
replies
254
views
bigWig size difference between variableStep and fixedStep wig files
bigWig
wig
1 day ago by
notthebmovieactor
• 0
0
votes
6
replies
236
views
Unannotated reads through STAR
STAR
IGV
Unannotated-reads
1 day ago by
rajdeepboral00
▴ 20
0
votes
2
replies
153
views
multiple outputfiles after bamtofastq for same library
cellranger
10x
bamtofastq
updated 2 days ago by
GenoMax
149k • written 2 days ago by
Tolga
▴ 30
0
votes
0
replies
112
views
Transforming diploid GT on male X and Y chromosome to haploid
VCF
genotype
gVCF
2 days ago by
Michaela
• 0
2
votes
6
replies
283
views
Hisat2 index genome
hisat2
9 hours ago by
frarodmar17
• 0
27
votes
22
replies
62k
views
22 follow
Public Electronic Health Records Database
database
written 11.8 years ago by
Abhi
★ 1.6k
1
vote
1
reply
138
views
Comparison of metabolic data between groups (WT vs KO)
metabolism
updated 2 days ago by
ATpoint
86k • written 2 days ago by
solene.vardon
• 0
1
vote
6
replies
255
views
Estimating mRNA Half-Life from Single Time Point Data Using mRNA/Ribo-seq Expression Data
regression
mRNA
RNA-seq
Ribo-seq
updated 1 day ago by
Ram
44k • written 2 days ago by
Ramya
• 0
0
votes
0
replies
126
views
Random effect model RNAseq
rma
metafor
2 days ago by
a.stef.44
▴ 10
2
votes
2
replies
209
views
Barley, alignment rates
barley
alignment-rate
updated 18 hours ago by
Ram
44k • written 2 days ago by
IrK
▴ 100
0
votes
0
replies
117
views
News:
Introduction to Python for biologists course
NGS
Python
Programming
2 days ago by
Physalia-courses
★ 2.6k
120,247 results • Page
1 of 2405
Recent Votes
Answer: ChIPSeeker not annotating with hg38, stuck on hg19
A: Locus Zoom Issuing "No valid markers in VCF file" on a VCF created in Plink 1.9
A: Error: vector memory exhausted (limit reached?) during Seurat integration datase
edgeR questions for use with cytometry counts
Answer: Combining Microarray and RNAseq data
Resources for flow cytometry bioinformatics
Answer: Comparing microarray to RNA-seq data
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Comment: Illumina HumanHT-12 V4.0 analysis but I only have the .IDAT files
by
isaac_mani
• 0
This is what I did after exporting my data from GenomeStudio although I personally think I did something wrong when exporting library(…
Answer: ChIPSeeker not annotating with hg38, stuck on hg19
by
John
• 0
Fixed it, I just opened a new R session and transferred my data frame over using these commands save as RDS saveRDS(my_dataframe, file = "…
Comment: Locus Zoom Issuing "No valid markers in VCF file" on a VCF created in Plink 1.9
by
alessandrotestori7
▴ 420
Thank you for your suggestion, I changed '.' to 'PASS' in the FILTER column and it worked
Comment: I can not obtain my counts in galaxy server
by
GenoMax
149k
Please post `galaxy` related question on their forum to get help: https://help.galaxyproject.org/ They can probably access your history (i…
Comment: Overlapping regions in bedGraph
by
Ram
44k
Sort the liftOver file and check for overlaps. lifeOver can be imprecise.
Comment: Illumina HumanHT-12 V4.0 analysis but I only have the .IDAT files
by
isaac_mani
• 0
I think so I got oonly AVG_SIGNAL and AVG.DETECTION_P-value for my three conditions
Comment: Umi_tools regex blank output
by
amyruthvandiver
• 0
Thank you SO much! I apologize for not catching that error.
Answer: How well was the rRNA depletion for RNA-Seq experiments
by
GenoMax
149k
> we would like to control for its efficiency. In this case you want to see how much rRNA is remaining in the samples? If so the `bbduk.sh…
Comment: Illumina HumanHT-12 V4.0 analysis but I only have the .IDAT files
by
GenoMax
149k
> I understand that I must extract fluorescence levels in the GenomeStudio analysis program Does it mean you have already done this part …
Answer: Analyze read lengths in Illumina data
by
Pierre Lindenbaum
165k
in the terminal, using **gnuplot**: $ gunzip -c in.fastq.gz | paste - - - - | awk -F '\t' '{print length($2);}' | sort | uniq -c …
Answer: Convert Long Nanopore reads to Illumina Paired end reads
by
Pierre Lindenbaum
165k
I just wrote jvarkit/biostar9608448 for fun. It takes a single-end bam and output a paire-end bam with reads having a length of 'x': https:…
Comment: Finding high number of significant genes by FindMarkers by Seurat
by
jared.andrews07
★ 18k
Nothing concrete, unfortunately. You can try some other methods (limma, edgeR), but you'll likely get pretty similar results. I'd try dropp…
Comment: Drosophila melanogaster dm3 intron percentage too high
by
Istvan Albert
102k
For dmel6, the genome size based on sequences contained in the FASTA is 143 million bp. The paper below reports the genome size to be 180 …
Answer: Analyze read lengths in Illumina data
by
GenoMax
149k
> a tool or method to calculate the number of reads for different lengths in a .fq.gz file. You could also run FastQC on the file. Once do…
Comment: Drosophila melanogaster dm3 intron percentage too high
by
GenoMax
149k
D. mel genome is supposed to be 180,000,000 bases.
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